Comparative Genomics

AMOL KUNDE Btech,Msc(ComputationalBiology) CORK INSTITUTE OF TECHNOLOGY,IRELAND

Comparative Genomics

Two very large problems are immediately apparent in undertaking the

sequencing of entire genomes.

First, the vast numbers of species and the much larger size of some

genomes makes the entire sequencing of all genomes a non-optimal

approach for understanding genome structure.

Second, within a given species most individuals are genetically distinct in

a number of ways. What does it actually mean, for example, to "sequence

a human genome"? The genomes of two individuals who are genetically

distinct differ with respect to DNA sequence by definition.

These two problems, and the potential for other novel applications, have given

rise to new approaches which, taken together, constitute the field of

comparative genomics.

Definition• Comparative genomics is the study of the relationship of genome structure and function

across different biological species or strains.• The purpose is to gain a better understanding of how species have evolved and to determine

the function of genes and noncoding regions of the genome.

GeneScan :Algorithm For Comparative Genomics

Uses Fourier technique based on a distinctive feature of protein-coding regions.

Sequence :GGATACACTTTAGAG       Apply UA 001010100001010       Apply UT 000100001110000        Converted into BinaryApply UG 110000000000101      Apply UC 000001010000000

where the discrete frequency f=k/N, with k=1,2,....N/2

The average of the total spectrum, S^, can be calculated from the frequency of occurrence

Tools

Interactive DAGchianer Algorithm:Tool for mining GenomeDuplication & Synteny

Finding putative genes or regions of homology between two genomes

Identifying collinear sets of genes or regions of sequence

Generating a dotplot of the results and coloring syntenic pairs.

Comparative Genomics Tool

Syntentic dotplot:  Syntentic dotplots give biologists very valuable information about how organisms diverged from a common ancestor.

Biologists can easily look at one of these dotplots and see where large sections of DNA have been deleted, inserted, copied, or moved.

The dotplots are also very good at depicting how closely two organisms are related through the quantity and linearity of green dots over an entire genome.

Summary

• Genes are complex structures which are difficult to predict with the required level of accuracy/ confidence

• Different approaches to gene finding improve accuracy/confidence of the predictions: